Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome

Abstract

Background: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. Methods: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. Results: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans

“…Many of these ARGs are encoded on the chromosome and have been often co-opted for AMR as an extension of general functions related to bacterial surivial. 17,49 In support of our findings, multidrug efflux pumps, resistant rpoB, and resistant topoisomerase have been detected in microbiomes of prehistoric humans, 23,50 providing additional evidence that these ARGs are ''ancient.'' 51…”

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

“…Finally palaeoproteomic analyses of palaeofaeces may offer new insight into community-level gut microbiome composition and function [ 71 ], which is complementary to ancient metagenomic approaches [ 35 ]. The gut microbiome is otherwise only preserved in mummified remains, and information from palaeofaeces is therefore a valuable contribution to the understanding of microbiome evolution.…”

“…R. Soc. B 288: 20210020 ancient metagenomic approaches [35]. The gut microbiome is otherwise only preserved in mummified remains, and information from palaeofaeces is therefore a valuable contribution to the understanding of microbiome evolution.…”

“…However, palaeoproteomic analyses have only been applied to the substrate with limited success [ 33 ]. Ancient DNA evidence has shown palaeofaeces to preserve dietary information as well as evidence of the gut microbiome [ 34 , 35 ], but the scope of these studies has been limited owing to its complex and highly degradable nature [ 32 ]. Furthermore, DNA studies are limited by a lack of tissue specificity, which is a major strength of palaeoproteomics.…”

Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens

“…Intestinal microbiome, including pathogens [94,96,98,99,101,140,[144][145][146][147] Helminths [86,87] Other: Birch pitch -Presence in the oral cavity/expression in saliva Epstein Barr virus, EBV (human gammaherpesvirus 4) [148] Other: Calcified nodules -Presence in genitourinary tissue…”